More is needed to move the spiritual concept of Heaven to a metaphysical naturalist 'heaven' (or physical heaven).
and let's further assume thay he or she comes in the form of a physicist who can explain what heaven is, be it Dark Matter or not, in terms consistent with physics, like what particles exist there; then in your mind has heaven been removed from the realm of the supernatural?
No. It's one thing to show that a planet Vulcan in M31 as being consistent with astronomy and physics, it's quite another to show that planet Vulcan is needed to account for our understanding of astronomy and physics. And, it's even a bigger jump to show that planet Vulcan actually exists even if it is needed to make the best explanation for our science. Just taking an advanced being's word for it that they came from Vulcan in M31 and this is what it is like is not enough to show that Vulcan is a requirement for our proper understanding of astronomy.
In my view, the Christ-like figure would need to produce physical evidence that is inescapable from reason. For example, we'd need a mathematical theory that cohered with our existing theories (i.e., we can derive an existing theories from this theory of heaven existing) and we need a number of predictions. Also, there must be no competing theories that are also rationally compelling.
After all under this premise, it is where God resides, according to the profound spiritual being.
That, I think, is not good enough. Testimony is acceptable if the results are duplicatable. For example, if we could send out a probe (after understanding the theory on how to do that) that was able to return showing physical evidence of God (e.g., the probe is able to interview God in a video, etc), then, in that case, it would be a perfectly acceptable for a methodological naturalist to propose the existence of a physical God to explain the data, etc. Of course, this still does not prove that God exists, it just shows that a methodological naturalist is justified in referring to God as an entity with respect to the new theoretical understanding that has physical evidence to back it up.
In that hypothetical case, in my opinion, God and Heaven become naturalist terms. The supernatural is no longer 'supernatural', but it has entered the naturalist domain.
Look at it this way. At one time magic was thought of as supernatural. If a few of us were to go back in time to the 15th century with our cell phones (assuming we could also transport cell towers and switching equipment to use those phones), and if we told those people that it is 'new magic', chances are they would believe us. There would be no chance that they would say that our cell phones are natural. Rather, they would most likely agree that we have our magic phones based on supernatural processes. Of course, our naive 15th century friends who might be getting ready to burn us at the stake would be incorrect about the magic and supernatural characteristics of cell phones.
In a similar way, if Heaven turned out to be a physical location that a future physical theory demanded that we refer to as 'existing' due to the preponderance of evidence, then I think that our current beliefs of Heaven as supernatural would fall into the same category as those hypothetical 15th century folks who were briefly exposed to cell phones. Even if those 15th century folks had a concept of cell phones as part of their religion prior to our arrival, the fact of the matter is that doesn't matter what they thought about cell phones as being supernatural (even if they had already a preconceived supernaturalist notion of cell phones) - the cell phones are part of a naturalist understanding of the world. They are not supernatural objects by the mere fact that their inner workings can be understood using a purely methodological naturalist approach.
Cell phones, or physical heaven, it wouldn't matter. If the criteria is met in order to reject the supernatural implications, then you have to reject it as supernatural. At least, that's my position. :-)